AMBER Archive (2009)

Subject: [AMBER] probelm-APBS

From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Date: Sat Oct 03 2009 - 00:41:07 CDT


Dear anyone who may concern this letter,

When I was using apbs to calculate the eletrostatic binding Energy, I found when:
   dime  240 240 240
       cglen 120 120 120
       fglen 90 90 90
       cgcent mol 1
       fgcent mol 1
That would be ok, but when I used the script:
dime  240 240 240

       cglen 120 120 120

       fglen 90 90 90

       cgcent mol 1

       fgcent mol 3,
there is following errors:
NOsh_setupCalcMGAUTO:  Error!  Finest mesh has fallen off the coarser meshes!
NOsh_setupCalcMGAUTO:  difference in min 1-direction = 0.3355
NOsh_setupCalcMGAUTO:  min fine = 32.546 -10.8485 6.95322e-310
NOsh_setupCalcMGAUTO:  min coarse = 6.44 -10.513 6.95314e-310
VASSERT: ASSERTION FAILURE!  filename nosh.c, line 1581, (0)
Aborted
I want to make the center of my grid as the cernter of the complex (mol1), then on the center of the ligand (mol3). I ever used this approach to calculate some other similar complex, to to this complex it does not work!

Can anyone give me some suggestions?

Rilei Yu

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